Another aspect could be related to past traumas. Naruto has been through a lot, and if the Konoha 11, even unintentionally, reminded him of some of the negative experiences he had in Konoha, like the ostracism he faced as a child, it could make him hate them in the fanfiction.
In some cases, it could be because the writer wants to deviate from the typical 'hero is loved' trope. They might think that exploring a scenario where Naruto is hated in his own village can bring out new aspects of his character. It could also be related to exploring the politics within the village. For example, perhaps there are factions in Konoha that see Naruto as a threat, either because of the Nine - Tails inside him or because they fear his growing power. This kind of fanfiction can dig deep into these political undercurrents.
In some fanfictions, Naruto might be depicted as hating Konoha due to feeling betrayed. For example, if the village turns against him unjustly or fails to support him when he needs it most. Maybe they suspect him of something he didn't do, like being involved in a crime against the village, which could lead to his hatred.
Another reason could be that he witnesses corruption or unfairness within the village leadership. If he sees that the system is rigged against certain groups, including himself or his friends, he could grow to hate Konoha and decide to leave.
Perhaps she witnessed some dark secrets of Konoha that made her lose faith in the village. It could be something related to the way the village leadership handled certain events or treated some of its people unfairly.
One common theme could be Naruto feeling betrayed by Konoha. Maybe he discovers some dark secrets about the village that make him turn against it. For example, if he found out that the village was using shinobi unfairly or was involved in immoral activities.
In some fanfics, Naruto might be depicted as hating Konoha. This could be due to various reasons like feeling betrayed by the village's hidden agendas or being mistreated in some alternate storylines.
Perhaps she discovers some dark secrets about Konoha's past. Things like the way the village treated certain clans or individuals unfairly. If she uncovers that Konoha was involved in some unethical actions in the past, it could make her lose faith in and start to hate the village. Also, if her loved ones were wrongly treated or sacrificed by Konoha's decisions, that would be a strong reason.
One reason could be false accusations. If Naruto is wrongly accused of a major crime in the village and no one believes him, he might start to hate Konoha.
Some fans create these stories because they want to explore different aspects of Naruto's character. By making him hate Konoha, they can show his growth in a different light, one that is not bound by his loyalty to the village.